The testing plugin is enabled and should be disabled.

You are here: index » tutorials » impact_oct_09

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

tutorials:impact_oct_09 [2015/09/16 14:54]
hafsa [The Genome summary] 		tutorials:impact_oct_09 [2015/09/17 10:48] (current)
hafsa [The Genome comparison page]
Line 41: Line 41:
 The first step is to go to the CATH home page (http://www.cathdb.info/) and just take a quick look. To the right hand side you can find a column of boxes with links to new developments in CATH. Other links to useful information (references, search tools) can be found in the main part of page, as well as in the footer, which is found at the bottom of every page. Up in the top right you can find links to the key functions of the web site and the ‘Quick Search’ box. This is where we are going to start. Enter the PDB code 1gcq into this box and hit the button (or the ‘Enter’ key). The first step is to go to the CATH home page (http://www.cathdb.info/) and just take a quick look. To the right hand side you can find a column of boxes with links to new developments in CATH. Other links to useful information (references, search tools) can be found in the main part of page, as well as in the footer, which is found at the bottom of every page. Up in the top right you can find links to the key functions of the web site and the ‘Quick Search’ box. This is where we are going to start. Enter the PDB code 1gcq into this box and hit the button (or the ‘Enter’ key).
  
-[[http://www.cathdb.info/cgi-bin/search.pl?search_text=1gcq#TabResults|Direct link to Results]]+[[http://www.cathdb.info/search/by_text?q=1gcq|Direct link to Results]]
  
 In a CATH results page all the records that may correspond to the query term are returned. The possible return types are ‘Domain’, ‘Chain’, ‘PDB’ and ‘Node’. Node corresponds to a node in the CATH structural hierarchy, i.e. a superfamily. It is worth noting that a CATH domain code is an extension of the PDB Chain identifier (i.e. 1gcqA00 is a domain in chain 1gcqA, which is found in record 1gcq). In a CATH results page all the records that may correspond to the query term are returned. The possible return types are ‘Domain’, ‘Chain’, ‘PDB’ and ‘Node’. Node corresponds to a node in the CATH structural hierarchy, i.e. a superfamily. It is worth noting that a CATH domain code is an extension of the PDB Chain identifier (i.e. 1gcqA00 is a domain in chain 1gcqA, which is found in record 1gcq).
Line 118: Line 118:
 We can find a summary of a superfamily  by searching from the "Get superfamily summary" tab on the front page. We can find a summary of a superfamily  by searching from the "Get superfamily summary" tab on the front page.
 For example searching for 2.40.128.20 we can see information on functions, domain partners, genome distributions etc For example searching for 2.40.128.20 we can see information on functions, domain partners, genome distributions etc
-[[http://gene3d.biochem.ucl.ac.uk/superfamily/2.40.128.20|Direct link to Results]].+[[http://gene3d.biochem.ucl.ac.uk/search?sterm=+2.40.128.20&mode=family|Direct link to Results]].
 If we click on the Domain organisation tab we can see different domain combinations and the organisms they are found in. If we click on the Domain organisation tab we can see different domain combinations and the organisms they are found in.
  
Line 134: Line 134:
 We can compare 2 genomes by searching from the "Compare Genomes" tab on the front page. We can compare 2 genomes by searching from the "Compare Genomes" tab on the front page.
 For example lets compare the human pathogen plasmodium vivax and the more lethal species plasmodium falciparum. For example lets compare the human pathogen plasmodium vivax and the more lethal species plasmodium falciparum.
-[http://gene3d.biochem.ucl.ac.uk/genome/comparison?db=ensembl&taxon-1=PLASMODIUM+FALCIPARUM+3D7&taxon-2=PLASMODIUM+VIVAX|Direct link to Results]].+[[http://gene3d.biochem.ucl.ac.uk/compareTaxons?taxon1=PLASMODIUM+VIVAX&taxon2=PLASMODIUM+FALCIPARUM+3D7&mode=genome|Direct link to Results]].
 we can click on individual tabs to see superfamilies, funfams and domain organisations compared between the 2 genomes by their counts of proteins between the two species. we can click on individual tabs to see superfamilies, funfams and domain organisations compared between the 2 genomes by their counts of proteins between the two species.
 For example on the funfams tab we can see that the "Rifin -like domain" is found in several sequences in P.falciparum and is absent from p.vivax. For example on the funfams tab we can see that the "Rifin -like domain" is found in several sequences in P.falciparum and is absent from p.vivax.

Trace:

Print/export